[R-sig-Geo] Trouble installing rgdal

[Gabor Grothendieck]

I am having trouble install rgdal. I am using
Red Hat Enterprise Linux Server release 5.5 (Tikanga)
and having the problem shown below when I try to install
rgdal.

I have previously installed rgdal including building gdal
from source so I am not new to this but have not previouly
installed it on this particular machine.

I built gdal 1.7.2 from source (couldn't get it going otherwise) using
this configure command:
./configure --with-sqlite3=internal --without-libtool
--without-ld-shared --with-expat=/usr/local/lib

These commands all run ok so I assume gdal did get installed:

gdal_translate --version
gdalwarp --formats
gdal-config --version

All the switches on the above configure seemed to be essential
or else it would not build or run.  Maybe the problem is that
I had to configure it using --without-ld-shared but rgdal uses
-shared in its build.  How can I change that?  Or is there something
else I can do?


> install.packages("rgdal")
...snip...
checking proj_api.h presence... yes
checking for proj_api.h... yes
checking for pj_init_plus in -lproj... yes
./proj_conf_test: error while loading shared libraries: libproj.so.0:
wrong ELF class: ELFCLASS32
./proj_conf_test: error while loading shared libraries: libproj.so.0:
wrong ELF class: ELFCLASS32
Package CPP flags: -I/usr/local/include
Package LIBS: /usr/local/lib/libgdal.a -Linternal/lib -lsqlite3
-L/usr/local/lib/lib -lexpat -lgif -ljpeg -ltiff -lpng -lz -lm -lrt
-ldl -L/usr/kerberos/lib64 -lcurl -ldl -lgssapi_krb5 -lkrb5 -lk5crypto
-lcom_err -lidn -lssl -lcrypto -lz
configure: creating ./config.status
config.status: creating src/Makevars
** libs
g++ -m64 -I/usr/include/R -I/usr/local/include -I/usr/local/include
-I"/usr/lib64/R/library/sp/include"   -fpic  -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c OGR_write.cpp -o
OGR_write.o
g++ -m64 -I/usr/include/R -I/usr/local/include -I/usr/local/include
-I"/usr/lib64/R/library/sp/include"   -fpic  -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c gdal-bindings.cpp -o
gdal-bindings.o
gdal-bindings.cpp: In function ‘SEXPREC* RGDAL_GetRasterData(SEXPREC*,
SEXPREC*, SEXPREC*, SEXPREC*)’:
gdal-bindings.cpp:1016: warning: unused variable ‘offset’
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
-I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c local_stubs.c -o
local_stubs.o
g++ -m64 -I/usr/include/R -I/usr/local/include -I/usr/local/include
-I"/usr/lib64/R/library/sp/include"   -fpic  -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c ogr_geom.cpp -o
ogr_geom.o
gcc -m64 -std=gnu99 -I/usr/include/R -I/usr/local/include
-I/usr/local/include -I"/usr/lib64/R/library/sp/include"   -fpic  -O2
-g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c ogr_polygons.c -o
ogr_polygons.o
g++ -m64 -I/usr/include/R -I/usr/local/include -I/usr/local/include
-I"/usr/lib64/R/library/sp/include"   -fpic  -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c ogr_proj.cpp -o
ogr_proj.o
g++ -m64 -I/usr/include/R -I/usr/local/include -I/usr/local/include
-I"/usr/lib64/R/library/sp/include"   -fpic  -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c ogrdrivers.cpp -o
ogrdrivers.o
g++ -m64 -I/usr/include/R -I/usr/local/include -I/usr/local/include
-I"/usr/lib64/R/library/sp/include"   -fpic  -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c ogrsource.cpp -o
ogrsource.o
g++ -m64 -I/usr/include/R -I/usr/local/include -I/usr/local/include
-I"/usr/lib64/R/library/sp/include"   -fpic  -O2 -g -pipe -Wall
-Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
--param=ssp-buffer-size=4 -m64 -mtune=generic -c projectit.cpp -o
projectit.o
projectit.cpp: In function ‘SEXPREC* projInfo(SEXPREC*)’:
projectit.cpp:301: warning: ‘ans’ may be used uninitialized in this function
g++ -m64 -shared -L/usr/local/lib64 -o rgdal.so OGR_write.o
gdal-bindings.o local_stubs.o ogr_geom.o ogr_polygons.o ogr_proj.o
ogrdrivers.o ogrsource.o projectit.o /usr/local/lib/libgdal.a
-Linternal/lib -lsqlite3 -L/usr/local/lib/lib -lexpat -lgif -ljpeg
-ltiff -lpng -lz -lm -lrt -ldl -L/usr/kerberos/lib64 -lcurl -ldl
-lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lidn -lssl -lcrypto -lz
-lproj -L/usr/lib64/R/lib -lR
/usr/bin/ld: /usr/local/lib/libgdal.a(genbindataset.o): relocation
R_X86_64_32 against `a local symbol' can not be used when making a
shared object; recompile with -fPIC
/usr/local/lib/libgdal.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [rgdal.so] Error 1
ERROR: compilation failed for package ‘rgdal’
* removing ‘/usr/lib64/R/library/rgdal’

The downloaded packages are in
        ‘/tmp/RtmpglHU18/downloaded_packages’
Updating HTML index of packages in '.Library'
Warning message:
In install.packages("rgdal") :
  installation of package 'rgdal' had non-zero exit status